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# fmt: off
import numpy as np
import pytest
from ase.build import bulk
from ase.calculators.calculator import compare_atoms
from ase.io.amber import read_amber_coordinates, write_amber_coordinates
@pytest.mark.parametrize('with_velocities', [False, True])
def test_io_amber_coordinates(with_velocities):
atoms = bulk('Au', orthorhombic=True)
filename = 'amber.netcdf'
if with_velocities:
atoms.set_velocities(np.random.default_rng(42).random((len(atoms), 3)))
write_amber_coordinates(atoms, filename)
atoms2 = read_amber_coordinates(filename)
# The format does not save the species so they revert to 'X'
assert all(atoms2.symbols == 'X')
assert compare_atoms(atoms, atoms2) == ['numbers']
assert atoms.get_velocities() == pytest.approx(atoms2.get_velocities())
def test_cannot_write_nonorthorhombic():
atoms = bulk('Ti')
with pytest.raises(ValueError, match='Non-orthorhombic'):
write_amber_coordinates(atoms, 'xxx')
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